Tokyo and Washington agreed in 2011 to relocate a training site for US fighter jets to Mageshima island, around 30 kilometres off the southwestern Japanese coast.
Japan's chief cabinet secretary Yoshihide Suga said an agreement to purchase Mageshima was reached on Friday "after discussions between the defence ministry and the developer who owns the majority of the island".
American flight training operations are currently conducted at Iwo Jima, some 1,200 kilometres (750 miles) south of Tokyo.
Washington had requested a move, saying Iwo Jima -- a key World War II battlefield -- was too far away from an American military base in the western Japanese city of Iwakuni, where their fighters are stationed.
Suga said a facility would be built on the island for landing practice "at an early date", adding that he could not reveal further details as the acquisition was not complete.
Japan's military has long been restricted to self-defence and the country relies heavily on the US under a bilateral security alliance.
President Donald Trump has repeatedly insisted that Japan and other US allies should contribute more to the costs of their own defence.
Some residents who live on islands close to Mageshima have said they are concerned about the noise of a potential flight training base.
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